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Improved Integrated Quality Control

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@lacan lacan released this 05 Sep 07:54
· 90 commits to main since this release

This release builds on v0.4.0 #7365020 following comments by @romainGuiet to integrate the whole QC directly rather than run it separately (Which no-one will ever do until it's too late 😅).

Improvements

Quality control is perfomed after training provided that:

  1. You added the scikit-image dependency to your cellpose installation
  2. You copy run-cellpose-qc.py into your QuPath extensions folder

Read the updated ReadMe to see how to do these installation steps.
Here is an example gif in real time (only 100 epochs though)

cellposeValidation

Possibility to save the training graph as a PNG in your QuPath project's QC folder

On top of showing you the training graph if you request it after training using showTrainingGraph(),
you can also choose to save it but not show it using showTrainingGraph(boolean show, boolean save)

Updated JavaDoc and ReadMe to account for the new features

As ususal, JavaDoc is here: https://biop.github.io/qupath-extension-cellpose/qupath/ext/biop/cellpose

Always happy to receive comments and suggestions!